Maker-P: Tool For De-Novo Annotation and Management Of Plant Genomes

Recent advances in genome sequencing and assembly have greatly increased the numbers of sequenced, assembled, but still un-annotated plant genomes worldwide; likewise, RNA-seq data is creating many opportunities to both assess the quality of existing annotation datasets, and to update and improve them. The overarching goal of the MAKER-P project is to meet these needs by providing the plant-genomics community with an easy-to-use tool for annotation of new plant genomes, and for management of existing plant-genome annotation datasets. In order to benchmark the accuracy of MAKER–P as a de-novo annotation tool, we have re-annotated the Arabidopsis thaliana genome with MAKER-P using several different combinations of RNA-seq and protein datasets as external evidence.  Our results demonstrate that MAKER-P can achieve gene-level accuracies that exceed 90% when compared to the TAIR-10 dataset, and using only RNA-seq data. We will also present systematic analyses of the consistency of the TAIR-10 and MAKER-P annotations with RNA-seq and other datasets; and will show how MAKER-P can be used to rapidly update the TAIR-10 annotations as new RNA-seq data become available. We have also carried out similar analyses using the Zea mays genome and its annotations; and are in the midst of systematic analyses of the maize RefGen V2. & V3 gene-sets. Collectively, these analyses not only demonstrate the utility of MAKER-P for plant-genome annotation and management, they also provide novel, bird’s eye views of these essential plant-genomics resources.